# MetaQTL - Reference Manual

## Short Contents

- MetaQTL
- 1 Introduction
- 2 Data Base
- 3 Meta Analysis
- 4 Visualization
- 5 Utilities
- 6 Tutorial
- Appendix A Copying This Manual

## Table of Contents

- MetaQTL
- 1 Introduction
  - 1.1 General Overview
    - 1.1.1 What is MetaQTL
    - 1.1.2 Definition of the Problem
  - 1.2 Citing MetaQTL
  - 1.3 How to Get and Install MetaQTL
  - 1.4 Getting Help
  - 1.5 General Usage of the Programs
  - 1.6 References
- 2 Data Base
  - 2.1 Overview
    - 2.1.1 Experiment Table
    - 2.1.2 Trait Ontology Table
    - 2.1.3 GLMdb
    - 2.1.4 QTLdb
  - 2.2 MetaDB
    - 2.2.1 Command Line Options
- 3 Meta Analysis
  - 3.1 Consensus map
    - 3.1.1 InfoMap
      - 3.1.1.1 Method
      - 3.1.1.2 Command Line Options
      - 3.1.1.3 Output
    - 3.1.2 ConsMap
      - 3.1.2.1 Method
      - 3.1.2.2 Command Line Options
    - 3.1.3 Output
  - 3.2 QTL Projection
    - 3.2.1 Method
    - 3.2.2 QTLProj
      - 3.2.2.1 Command Line Options
      - 3.2.2.2 Output files
  - 3.3 QTL Clustering
    - 3.3.1 ClustQTL
      - 3.3.1.1 Method
      - 3.3.1.2 Command Line Options
      - 3.3.1.3 Output
    - 3.3.2 QTLTree
      - 3.3.2.1 Method
      - 3.3.2.2 Command Line Options
      - 3.3.2.3 Output
- 4 Visualization
  - 4.1 MapView
    - 4.1.1 Command Line Options
    - 4.1.2 Drawing Parameters
  - 4.2 MMapView
    - 4.2.1 Command Line Options
    - 4.2.2 Drawing parameters
  - 4.3 MQTLView
    - 4.3.1 Command Line Options
- 5 Utilities
  - 5.1 A2Xml
    - 5.1.1 Command Line Options
  - 5.2 Xml2A
    - 5.2.1 Command Line Options
  - 5.3 QTLClustInfo
    - 5.3.1 Command Line Options
  - 5.4 QTLModel
    - 5.4.1 Command Line Options
  - 5.5 References
- 6 Tutorial
  - 6.1 Tutorial Introduction
  - 6.2 Step 1 - Creating the XML Database
  - 6.3 Step 2 - Building the consensus map
    - 6.3.1 Checking chromosome connection and marker order consistency
    - 6.3.2 Building the consensus map
  - 6.4 Step 3 - Projection of the QTL
  - 6.5 Step 4 - QTL Clustering
    - 6.5.1 QTL Clustering
    - 6.5.2 QTL Tree
  - 6.6 Step 4 - Post processing
    - 6.6.1 Extracting the meta-QTL
    - 6.6.2 Projection of the meta-QTL
- Appendix A Copying This Manual
  - ADDENDUM: How to use this License for your documents

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## MetaQTL

Copyright © 2005 Jean-Baptiste Veyrieras, INRA.

> Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.2 or any later version published by the Free Software Foundation; with the Invariant Sections being "GNU General Public License" and "Free Software Needs Free Documentation", the Front-Cover text being “A GNU Manual”, and with the Back-Cover Text being (a) (see below). A copy of the license is included in the section entitled “GNU Free Documentation License”.

> (a) The Back-Cover Text is: “You have freedom to copy and modify this GNU Manual, like GNU software. Copies published by the Free Software Foundation raise funds for GNU development.”